Transition state theory, transmission

BINDING CHANGE MECHANISM TRANSMISSION COEFFICIENT TRANSITION STATE THEORY TRANSMISSION DENSITY TRANSMITTANCE TRANSMITTANCE... 

The quasi-equilibrium assumption in the above canonical fonn of the transition state theory usually gives an upper bound to the real rate constant. This is sometimes corrected for by multiplying (A3.4.98) and (A3.4.99) with a transmission coefifiwient 0 < k < 1. 

Voth G A 1990 Analytic expression for the transmission coefficient in quantum mechanical transition state theory Chem. Phys. Lett. 170 289... 

There is still some debate regarding the form of a dynamical equation for the time evolution of the density distribution in the 9 / 1 regime. Fortunately, to evaluate the rate constant in the transition state theory approximation, we need only know the form of the equilibrium distribution. It is only when we wish to obtain a more accurate estimate of the rate constant, including an estimate of the transmission coefficient, that we need to define the system s dynamics. 

Transition state theory, 46,208 Transmission factor, 42,44-46,45 Triosephosphate isomerase, 210 Trypsin, 170. See also Trypsin enzyme family active site of, 181 activity of, steric effects on, 210 potential surfaces for, 180 Ser 195-His 57 proton transfer in, 146, 147 specificity of, 171 transition state of, 226 Trypsin enzyme family, catalysis of amide hydrolysis, 170-171. See also Chymotrypsin Elastase Thrombin Trypsin Plasmin Tryptophan, structure of, 110... 

Various statistical treatments of reaction kinetics provide a physical picture for the underlying molecular basis for Arrhenius temperature dependence. One of the most common approaches is Eyring transition state theory, which postulates a thermal equilibrium between reactants and the transition state. Applying statistical mechanical methods to this equilibrium and to the inherent rate of activated molecules transiting the barrier leads to the Eyring equation (Eq. 10.3), where k is the Boltzmann constant, h is the Planck s constant, and AG is the relative free energy of the transition state [note Eq. (10.3) ignores a transmission factor, which is normally 1, in the preexponential term]. 

We begin our discussion with path integral quantum transition state theory (QTST) [14], which is the theoretical model that we use to model enzymatic reactions. In QTST, the exact rate constant is expressed by the QTST rate constant, qtst, multiplied by a transmission coefficient yq ... 

The Marcus classical free energy of activation is AG , the adiabatic preexponential factor A may be taken from Eyring s Transition State Theory as (kg T /h), and Kel is a dimensionless transmission coefficient (0 < k l < 1) which includes the entire efiFect of electronic interactions between the donor and acceptor, and which becomes crucial at long range. With Kel set to unity the rate expression has only nuclear factors and in particular the inner sphere and outer sphere reorganization energies mentioned in the introduction are dominant parameters controlling AG and hence the rate. It is assumed here that the rate constant may be taken as a unimolecular rate constant, and if needed the associated bimolecular rate constant may be constructed by incorporation of diffusional processes as ... 

Heat diffusivity transmission coefficient in the transition-state theory... 

In the very short time limit, q (t) will be in the reactants region if its velocity at time t = 0 is negative. Therefore the zero time limit of the reactive flux expression is just the one dimensional transition state theory estimate for the rate. This means that if one wants to study corrections to TST, all one needs to do munerically is compute the transmission coefficient k defined as the ratio of the numerator of Eq. 14 and its zero time limit. The reactive flux transmission coefficient is then just the plateau value of the average of a unidirectional thermal flux. Numerically it may be actually easier to compute the transmission coefficient than the magnitude of the one dimensional TST rate. Further refinements of the reactive flux method have been devised recently in Refs. 31,32 these allow for even more efficient determination of the reaction rate. 

TCLP TDB TDF THC TBP TEM TLM TM-AFM TOC TRLFS TRU TSP TST TVS Toxicity characteristics leaching procedure Thermodynamic database Tyre-derived fuel Total hydrocarbon Tri-n-butyl phosphate Transmission electron microscopy Triple layer model Tapping mode atomic force microscopy Total organic carbon Time-resolved laser fluorescence spectroscopy Transuranic Total suspended particles Transition state theory Transportable vitrification system... 

According to transition state theory, if the transmission coefficient k = 1, T and ET will be transformed to products at the same rate. Thus, if the mechanisms of the nonenzymatic and enzymatic reactions are assumed the same, the ratio of maximum velocities for first-order transformation of ES and S will be given by Eq. 9-85. For some enzymes the ratio... 

Transition state theory (Chapter 2, section A) was derived for chemical bonds that obey quantum theory. An equation analogous to that for transition state theory may be derived even more simply for protein folding because classical low energy interactions are involved and we can use the Boltzmann equation to calculate the fraction of molecules in the transition state i.e., = exp(— AG -D/RT), where A G D is the mean difference in energy between the conformations at the saddle point of the reaction and the ground state. Then, if v is a characteristic vibration frequency along the reaction coordinate at the saddle point, and k is a transmission coefficient, then... 

These relaxation times correspond to rates which are about 106 slower than the thermal vibrational frequency of 6 x 1012 sec 1 (kBT/h) obtained from transition state theory. The question arises how much, if any, of this free energy of activation barrier is due to the spin-forbidden nature of the AS = 2 transition. This question is equivalent to evaluating the transmission coefficient, k, that is, to assess quantitatively whether the process is adiabatic or nonadiabatic. 

Thus k is the transmission coefficient that measures deviation of the Grote-Hynes rate kGH from the transition state theory rate kTST. 

Transition-state theory is based on two assumptions, the existence of both a dynamic bottleneck and a preceding equilibrium between a transition-state complex and reactants. Eq. (2.4) results, where k denotes the observed reaction rate constant, k the transmission coefficient, and v the mean frequency of crossing the barrier. 

In Kramers theory that is based on the Langevin equation with a constant time-independent friction constant, it is found that the rate constant may be written as a product of the result from conventional transition-state theory and a transmission factor. This factor depends on the ratio of the solvent friction (proportional to the solvent viscosity) and the curvature of the potential surface at the transition state. In the high friction limit the transmission factor goes toward zero, and in the low friction limit the transmission factor goes toward one. 

The transmission coefficient kgh is, as previously, a measure of the departure of the rate constant from transition-state theory, kqh is given as the ratio between the frequencies with and without friction, that is,... 

According to transition-state theory it is possible to consider reaction velocities in terms of a hypothetical equilibrium between reactants and transition state. It follows that the influence of the isotopic composition of the medium on reaction velocity can be considered to be the same as its influence on the concentration of transition states. The kinetic formulation of the problem can thus be replaced by one couched in equilibrium terms, and the equilibrium theory of the preceding section can be applied with a minimum of modification (Kresge, 1964). The rate constant, or catalytic coefficient, (k) for a catalysed reaction can be written as the product of three factors, viz. the equilibrium constant (K ) for the process forming the transition state from the reactants, the transmission coefficient, and the specific rate of transition state decomposition (kT/h). We recognize that the third factor is independent of the isotopic nature of the reaction and assume that there is no isotope effect on the transmission coefficient. It follows that... 

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